Error when running Stage 30 in the Quickstart Tutorial

[astrobel]

Hi,

I'm currently working through the Quickstart Tutorial and come across the following error when running Stage 30. I have not altered any parameters in the PCF from the example.

Here's the output & error:

workdir:  ./run_2022-10-19_11-54-11_GJ1214_Hubble13021/
eventlabel:  GJ1214_Hubble13021
Successfully reloaded meta file
Starting s30
Spectroscopic light curve fit(s) will be performed
using most recent s21 run: ./run_2022-10-19_11-54-11_GJ1214_Hubble13021//extracted_sp/bins11_2022-10-19_12-12-10
Identified file(s) for fitting: ['./run_2022-10-19_11-54-11_GJ1214_Hubble13021//extracted_sp/bins11_2022-10-19_12-12-10/speclc1.158.txt', './run_2022-10-19_11-54-11_GJ1214_Hubble13021//extracted_sp/bins11_2022-10-19_12-12-10/speclc1.204.txt', './run_2022-10-19_11-54-11_GJ1214_Hubble13021//extracted_sp/bins11_2022-10-19_12-12-10/speclc1.250.txt', './run_2022-10-19_11-54-11_GJ1214_Hubble13021//extracted_sp/bins11_2022-10-19_12-12-10/speclc1.296.txt', './run_2022-10-19_11-54-11_GJ1214_Hubble13021//extracted_sp/bins11_2022-10-19_12-12-10/speclc1.342.txt', './run_2022-10-19_11-54-11_GJ1214_Hubble13021//extracted_sp/bins11_2022-10-19_12-12-10/speclc1.389.txt', './run_2022-10-19_11-54-11_GJ1214_Hubble13021//extracted_sp/bins11_2022-10-19_12-12-10/speclc1.435.txt', './run_2022-10-19_11-54-11_GJ1214_Hubble13021//extracted_sp/bins11_2022-10-19_12-12-10/speclc1.481.txt', './run_2022-10-19_11-54-11_GJ1214_Hubble13021//extracted_sp/bins11_2022-10-19_12-12-10/speclc1.527.txt', './run_2022-10-19_11-54-11_GJ1214_Hubble13021//extracted_sp/bins11_2022-10-19_12-12-10/speclc1.573.txt', './run_2022-10-19_11-54-11_GJ1214_Hubble13021//extracted_sp/bins11_2022-10-19_12-12-10/speclc1.619.txt']

****** File: 1/11


Removed 8 exposures because they were the first exposures in the orbit.
Removed 34 exposures because they were the first orbit in the visit.
median log10 raw flux: 6.246165202239972
The highest amount of exposures in an orbit is 18
Number of free parameters:  21
Names of free parameters:  ['t0', 'rp', 'u1', 'c', 'c', 'c', 'v', 'v', 'v', 'r1', 'r1', 'r1', 'r2', 'r2', 'r2', 'r3', 'r3', 'r3', 'scale', 'scale', 'scale']
The predicted rms is 247.26

*STARTS LEAST SQUARED*
Runs MPFIT... 
v_1      9.7091e-05      8.4716e-07
r2_0     1.1420e-05      6.5022e-10
r2_1     2.2779e-03      3.3807e-07
r3_0     6.2578e-05      5.5039e-09
r3_1     4.1557e-05      3.3397e-07
scale_0          2.8774e-02      7.4845e-05
scale_1          3.9560e-03      6.7583e-05
rms, chi2red =  267564.70429841534 1454721.5884296482
['t0', 'rp', 'u1', 'c0', 'c1', 'c0', 'v1', 'v0', 'v1', 'r10', 'r11', 'r10', 'r21', 'r20', 'r21', 'r30', 'r31', 'r30', 'scale1', 'scale0', 'scale1']

*STARTS MCMC*
Runs MPFIT... 
c_1      6.2841e+00      7.7178e-02
v_1      9.7091e-05      1.0218e-03
r2_0     1.6484e-05      1.1320e-06
r3_0     9.0327e-05      9.5821e-06
r3_1     1.7544e-01      1.8905e+00
scale_0          2.8774e-02      9.0272e-02
scale_1          3.9560e-03      8.1513e-02
rms, chi2red =  267564.70429854095 0.99999999999999
Traceback (most recent call last):
  File "/home/isy/aur/PACMAN/src/pacman/workdir/pacman_script.py", line 135, in <module>
    main()
  File "/home/isy/aur/PACMAN/src/pacman/workdir/pacman_script.py", line 131, in main
    meta = s30.run30(eventlabel, workdir)
  File "/home/isy/aur/PACMAN/src/pacman/s30_run.py", line 147, in run30
    val_mcmc, err_lower_mcmc, err_upper_mcmc, fit = mcmc_fit(data, model, params, f, meta, fit_par)
  File "/home/isy/aur/PACMAN/src/pacman/lib/mcmc.py", line 37, in mcmc_fit
    theta = util.format_params_for_sampling(params, meta, fit_par)
  File "/home/isy/aur/PACMAN/src/pacman/lib/util.py", line 706, in format_params_for_sampling
    theta = params[free_array]
IndexError: boolean index did not match indexed array along dimension 0; dimension is 46 but corresponding boolean dimension is 52

Thanks for any assistance you can provide!

[sebastian-zieba]

Hi Isabel,
thanks for the catch! I'll look into this today and tomorrow and get back to you!

[sebastian-zieba]

Hi,
the problem actually just lies in the fit_par.txt file. The template I have uploaded to GitHub is based on an old version of the documentation where I showed the user how to reduce and analyze three visits at once.

In order to save a bit on computational time and disk space, I rewrote the docs a few weeks ago to show the reduction and analysis of just two visits instead. I forgot to update the fit_par.txt file though.

I just uploaded a new version of the fit_par.txt file to GitHub: https://github.com/sebastian-zieba/PACMAN/blob/master/src/pacman/data/run_files/fit_par.txt
If you replace your fit_par.txt with this new one, it should all work out.

I also tweaked a few parameters in the pcf so that the user can run the Quickstart a bit quicker. I just decided to reduce the number of iterations performed by emcee when running this tutorial. If you want to save some time, you can adopt these changes too:

run_nsteps 4000
run_nwalkers 30
run_nburn 2000

Hope this helps!

[astrobel]

It's all working now, thanks so much @sebastian-zieba!!